Colour not filling whole of object
Check Faceorientation

Press Alt+V and select face orientation, the whole object should  be blue, means the faces are oriented the right way. Blue = outside, Red = inside.

Alternative model

Maybe it would be better to use a single vertex with some extrusions to shape branches, with modifiers shown in image bellow. To make parts thinner select the vertex and press ctrl+a
Something like this:

To get a more organic look add a lattice object. Select lattice and change the resolution.

Then add a lattice modifier to the tree-like-object. Note: Object has to be the lattice you created. After that, move vertices from the lattice in editmode.